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. 2011 Jun:Chapter 2:2.14.1-2.14.14.
doi: 10.1002/0471250953.bi0214s34.

Using MACS to identify peaks from ChIP-Seq data

Jianxing Feng  1 , Tao Liu  2 , Yong Zhang  1
Affiliations

Using MACS to identify peaks from ChIP-Seq data

Jianxing Feng et al. Curr Protoc Bioinformatics. 2011 Jun.

Abstract

Model-based Analysis of ChIP-Seq (MACS) is a command-line tool designed by X. Shirley Liu and colleagues to analyze data generated by ChIP-Seq experiments in eukaryotes, especially mammals. MACS can be used to identify transcription factor binding sites and histone modification-enriched regions if the ChIP-Seq data, with or without control samples, are given. This unit describes two basic protocols that provide detailed information on how to use MACS to identify either the binding sites of a transcription factor or the enriched regions of a histone modification with broad peaks. Furthermore, the basic ideas for the MACS algorithm and its appropriate usage are discussed.

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Figures

Figure 2.14.1
Figure 2.14.1
Shifting size model for FoxA1 ChIP-Seq data.
Figure 2.14.2
Figure 2.14.2
Visualization of wiggle and BED files for FoxA1 ChIP-Seq data in Affymetrix IGB. Genome region: chr1: 215,756,000 – 215,757,000.
Figure 2.14.3
Figure 2.14.3
Visualization of wiggle and BED files for H3K27me3 ChIP-Seq data in Affymetrix IGB. Genome region: chr1: 93,627,000 – 93,637,000.
See this image and copyright information in PMC

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